Subterranean ecosystems are regarded as the most extensive biome on earth, comprising terrestrial and aquatic systems - the latter constituting freshwater, anchialine and marine systems. This system plays a key role in the distribution and storage of freshwater, once it contains 97% of the world’s total liquid freshwater (Chapter 1), which has been progressively explored in quality and amount. Initial observation of the subterranean environment began with speleological studies by the recognition of a typical fauna adapted to live inside caves. The first studies to provide information about aquatic subterranean fauna commenced in Slovenia, with the description of the Proteus aguinus by Laurenti in 1768. After an initial faunal classification by the Danish zoologist Schiödte (1849), the Austrian naturalist Schiner (1854) established the most commonly used classification for cave fauna and a great portion of modern research dealing with ecobilogy of aquatic subterranean fauna has mostly evolved from the European biospeleology (Chapters 1 and 3). Studies in biospeleology have made a significant contribution to the progressive knowledge in aquatic subterranean ecology, especially in those circumstances where the access of the underground through smaller voids (e.g. crevicular spaces) is not possible. Accessibility to the underground environment is in fact a negative factor that has led a large number of studies consider about subterranean fauna initially being limited to caves. Spatial constraint was (and still is) a limiting factor in accessing a diverse range of subsurface habitats, although during the last decade, modern research has been using advance technology as a tool to overcome the physical barriers to subterranean research. For a long time the classification of subterranean aquatic organisms was an unclear subject, with the classification subterranean fauna mostly related to terrestrial cave fauna (troglofauna). The classification system dealing with aquatic subterranean groups (stygofauna) is more recent. A few nomenclature schemes have been proposed to describe these relationships, based on morphological, behavioural, and ecological adaptations of animals to the underground life and their level of relationship with groundwater (Chapter 4). The prefix “stygo” is suggested as the most descriptive to refer ecologically to a group of animals related to groundwater habitats. Groundwater related fauna (stygofauna) is comprised by groups of animals encompassing aquatic surface, intermediate and subterranean habitats. They represent diverse group of animals that have different interactive relationships with the groundwater habitat. Some may transact between surface water and groundwater systems, while others spend the whole life cycle in the subterranean voids (Gibert et al., 1994). This transition zone between surface streams and groundwater is recognized as a critically important boundary or ecotone, constituted by a habitat that contains a reservoir of invertebrate fauna biodiversity. It is therefore from the study of karst systems that most information on groundwater ecobiology is resourced, once the open structure of most karsts terrains promotes a number of caves, streams, crevices, sinkholes, and springs to allow human access. Karst systems are well fractured because of the relation between the rock mass and the action of meteoric water, as well as the dissolution rate of calcium carbonate rocks that high. The latter increases with time, producing a terrain with a great drainage potential (Chapter 2). Once porosity is high and the flow of percolating water is fast, it allows good vagility for subterranean fauna and nutrients, as well as penetration of contaminants. In subterranean karsts, much water saturates some areas inside rock spaces. The saturation in the rock in turn promotes large water pockets, known as aquifers. When these groundwater aquifers are found to be interconnecting with the adjacent ecosystems, they became active eco-hydrological components, due to their key participation in the surface-groundwater continuum. Groundwater has different degrees of importance, depending on the available sources of surface water. In many countries it supplies a significant proportion of urban and rural drinking water, industrial, and agricultural. Yet, groundwater systems are “hidden”, difficult in access and to study (Chapter 4, 5 and 7), consequently the recognition of the groundwater aquifer as a natural resource that needs to be protected is largely ignored. Moreover, studies in the ecobiology and distribution of stygobitic invertebrates (Chapter 5), and the need to identify a frame of methods for quality assessment and the suitability of groundwater invertebrates as bioindicative elements, has not been developed (Chapter 6). Finally, strong management and public education programs are required to emphasize the need for a better understanding of the nature of groundwater resources, their participation and complexity (Chapter 8), with the conceptualization of the groundwater aquifer integrity as an ecosystem still receiving little attention in South Africa.